AFAIK The position of the windows is not part of the work environment. Only the palettes are stored in the Palette Scheme (hence the name) and even then according to GS, not all palettes listed in the Windows> palettes menu are actually palettes!
I believe the position of the windows are stored with the actual project. If you set your template to have the windows positioned and sized the way you like, then use that template to start new projects they should stick. Similarly if you start a new project using the latest project settings, the windows in the new project will be same as the previous file.
I don't think there's any way to transfer window positions and sizes between projects, unless there's a preference or registry hack.
Dialog boxes are a different story though - their size and positions used to be stored in the ArchiCAD preferences, but even then they seem hit & miss (especially columns within dialogs). So that when you closed ArchiCAD (or the last instance if there were multiple instances open) the dialog boxes will were stored for next time. Not sure what's going on with them right now. I recall this being mentioned during beta testing, but looks like it wasn't fixed.
Cheers,
Link.